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. 2009 Sep;9(18):4276-83.
doi: 10.1002/pmic.200900402.

A guide to the Proteomics Identifications Database proteomics data repository

Juan Antonio Vizcaíno  1 , Richard Côté, Florian Reisinger, Joseph M Foster, Michael Mueller, Jonathan Rameseder, Henning Hermjakob, Lennart Martens
Affiliations
Free PMC article

A guide to the Proteomics Identifications Database proteomics data repository

Juan Antonio Vizcaíno et al. Proteomics. 2009 Sep.
Free PMC article

Abstract

The Proteomics Identifications Database (PRIDE, www.ebi.ac.uk/pride) is one of the main repositories of MS derived proteomics data. Here, we point out the main functionalities of PRIDE both as a submission repository and as a source for proteomics data. We describe the main features for data retrieval and visualization available through the PRIDE web and BioMart interfaces. We also highlight the mechanism by which tailored queries in the BioMart can join PRIDE to other resources such as Reactome, Ensembl or UniProt to execute extremely powerful across-domain queries. We then present the latest improvements in the PRIDE submission process, using the new easy-to-use, platform-independent graphical user interface submission tool PRIDE Converter. Finally, we speak about future plans and the role of PRIDE in the ProteomExchange consortium.

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Figures

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1
PRIDE Converter application graphical user interface. Screenshots from the PRIDE Converter application. The PRIDE XML file is created by completing eight simple steps. The OLS is used to provide experimental metadata annotation.
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Existing resources for the generation, validation and submission of PRIDE XML files. Schema showing the different tools and resources that can be used to submit data to PRIDE.
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